Construct Non-Hierarchical P/NBD Model for Short Timeframe Synthetic Data

In this workbook we construct the non-hierarchical P/NBD models on the CD-NOW transaction data.

1 Load and Construct Datasets

1.1 Load Short-Timeframe Synthetic Transaction Data

We now want to load the CD-NOW transaction data.

Code

customer_cohortdata_tbl <- read_rds("data/shortsynth_customer_cohort_data_tbl.rds")
customer_cohortdata_tbl |> glimpse()

Rows: 5,000
Columns: 5
$ customer_id     <chr> "SFC202001_0001", "SFC202001_0002", "SFC202001_0003", …
$ cohort_qtr      <chr> "2020 Q1", "2020 Q1", "2020 Q1", "2020 Q1", "2020 Q1",…
$ cohort_ym       <chr> "2020 01", "2020 01", "2020 01", "2020 01", "2020 01",…
$ first_tnx_date  <dttm> 2020-01-01 02:15:58, 2020-01-01 00:40:17, 2020-01-01 …
$ total_tnx_count <int> 3, 9, 1, 2, 5, 1, 4, 6, 2, 4, 1, 11, 3, 3, 1, 1, 11, 3…

Code

customer_transactions_tbl <- read_rds("data/shortsynth_transaction_data_tbl.rds")
customer_transactions_tbl |> glimpse()

Rows: 29,454
Columns: 7
$ customer_id   <chr> "SFC202001_0002", "SFC202001_0001", "SFC202001_0004", "S…
$ tnx_timestamp <dttm> 2020-01-01 00:40:17, 2020-01-01 02:15:58, 2020-01-01 18…
$ tnx_dow       <fct> Wed, Wed, Wed, Wed, Thu, Thu, Thu, Thu, Thu, Thu, Thu, F…
$ tnx_month     <fct> Jan, Jan, Jan, Jan, Jan, Jan, Jan, Jan, Jan, Jan, Jan, J…
$ tnx_week      <chr> "00", "00", "00", "00", "00", "00", "00", "00", "00", "0…
$ invoice_id    <chr> "T20200101-0001", "T20200101-0002", "T20200101-0003", "T…
$ tnx_amount    <dbl> 51.73, 139.05, 11.72, 88.30, 1.16, 0.95, 127.85, 35.07, …

Code

customer_subset_id <- read_rds("data/shortsynth_customer_subset_ids.rds")
customer_subset_id |> glimpse()

 Factor w/ 5000 levels "SFC202001_0002",..: 2 3 8 10 14 16 17 21 25 27 ...

We re-produce the visualisation of the transaction times we used in previous workbooks.

Code

plot_tbl <- customer_transactions_tbl |>
  group_nest(customer_id, .key = "cust_data") |>
  filter(map_int(cust_data, nrow) > 3) |>
  slice_sample(n = 30) |>
  unnest(cust_data)

ggplot(plot_tbl, aes(x = tnx_timestamp, y = customer_id)) +
  geom_line() +
  geom_point() +
  labs(
      x = "Date",
      y = "Customer ID",
      title = "Visualisation of Customer Transaction Times"
    ) +
  theme(axis.text.y = element_text(size = 10))

1.2 Load Derived Data

Code

obs_fitdata_tbl   <- read_rds("data/shortsynth_obs_fitdata_tbl.rds")
obs_validdata_tbl <- read_rds("data/shortsynth_obs_validdata_tbl.rds")

customer_fit_stats_tbl <- obs_fitdata_tbl |>
  rename(x = tnx_count)

1.3 Load Subset Data

We also want to construct our data subsets for the purposes of speeding up our valuations.

Code

customer_fit_subset_tbl <- obs_fitdata_tbl |>
  filter(customer_id %in% customer_subset_id)

customer_fit_subset_tbl |> glimpse()

Rows: 1,000
Columns: 6
$ customer_id    <fct> SFC202001_0001, SFC202001_0004, SFC202001_0008, SFC2020…
$ first_tnx_date <dttm> 2020-01-01 02:15:58, 2020-01-01 18:04:32, 2020-01-02 1…
$ last_tnx_date  <dttm> 2020-02-20 14:43:57, 2020-01-10 17:49:12, 2020-07-17 0…
$ tnx_count      <dbl> 2, 1, 5, 4, 0, 10, 10, 0, 0, 0, 6, 2, 0, 0, 0, 1, 0, 3,…
$ t_x            <dbl> 7.2170614, 1.2841927, 28.0650995, 12.3070761, 0.0000000…
$ T_cal          <dbl> 104.4151, 104.3210, 104.1918, 104.1751, 104.0693, 104.0…

Code

customer_valid_subset_tbl <- obs_validdata_tbl |>
  filter(customer_id %in% customer_subset_id)

customer_valid_subset_tbl |> glimpse()

Rows: 1,000
Columns: 3
$ customer_id       <fct> SFC202001_0001, SFC202001_0004, SFC202001_0008, SFC2…
$ tnx_count         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ tnx_last_interval <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …

We now use these datasets to set the start and end dates for our various validation methods.

Code

dates_lst <- read_rds("data/shortsynth_simulation_dates.rds")

use_fit_start_date <- dates_lst$use_fit_start_date
use_fit_end_date   <- dates_lst$use_fit_end_date

use_valid_start_date <- dates_lst$use_valid_start_date
use_valid_end_date   <- dates_lst$use_valid_end_date

Before we start on that, we set a few parameters for the workbook to organise our Stan code.

Code

stan_modeldir <- "stan_models"
stan_codedir  <-   "stan_code"

2 Fit First P/NBD Model

We now construct our Stan model and prepare to fit it with our synthetic dataset.

We also want to set a number of overall parameters for this workbook

To start the fit data, we want to use the 1,000 customers. We also need to calculate the summary statistics for the validation period.

2.1 Compile and Fit Stan Model

We now compile this model using CmdStanR.

Code

pnbd_fixed_stanmodel <- cmdstan_model(
  "stan_code/pnbd_fixed.stan",
  include_paths =   stan_codedir,
  pedantic      =           TRUE,
  dir           =  stan_modeldir
  )

We then use this compiled model with our data to produce a fit of the data.

Code

stan_modelname <- "pnbd_short_fixed1"
stanfit_seed   <- stanfit_seed + 1
stanfit_prefix <- str_c("fit_", stan_modelname) 

stanfit_object_file <- glue("data/{stanfit_prefix}_stanfit.rds")

stan_data_lst <- customer_fit_stats_tbl |>
  select(customer_id, x, t_x, T_cal) |>
  compose_data(
    lambda_mn = 0.25,
    lambda_cv = 1.00,
    
    mu_mn     = 0.10,
    mu_cv     = 1.00,
    )

if(!file_exists(stanfit_object_file)) {
  pnbd_short_fixed1_stanfit <- pnbd_fixed_stanmodel$sample(
    data            =                stan_data_lst,
    chains          =                            4,
    iter_warmup     =                          500,
    iter_sampling   =                          500,
    seed            =                 stanfit_seed,
    save_warmup     =                         TRUE,
    output_dir      =                stan_modeldir,
    output_basename =               stanfit_prefix,
    )
  
  pnbd_short_fixed1_stanfit$save_object(stanfit_object_file, compress = "gzip")

} else {
  pnbd_short_fixed1_stanfit <- read_rds(stanfit_object_file)
}

pnbd_short_fixed1_stanfit$summary()

# A tibble: 9,961 × 10
   variable       mean   median      sd     mad       q5      q95  rhat ess_bulk
   <chr>         <num>    <num>   <num>   <num>    <num>    <num> <num>    <num>
 1 lp__       -5.15e+4 -5.15e+4 63.9    63.9    -5.16e+4 -5.14e+4  1.01     675.
 2 lambda[1]   4.38e-1  4.22e-1  0.160   0.154   2.09e-1  7.26e-1  1.00    2471.
 3 lambda[2]   2.09e-1  1.79e-1  0.133   0.114   4.80e-2  4.60e-1  1.00    2548.
 4 lambda[3]   2.67e-1  2.13e-1  0.217   0.171   3.55e-2  7.23e-1  1.00    1821.
 5 lambda[4]   1.34e-1  7.62e-2  0.161   0.0895  3.51e-3  4.62e-1  1.00    1605.
 6 lambda[5]   4.88e-1  4.35e-1  0.262   0.241   1.60e-1  9.77e-1  1.00    2233.
 7 lambda[6]   2.47e-1  1.96e-1  0.199   0.163   3.29e-2  6.35e-1  1.00    1990.
 8 lambda[7]   1.44e-1  8.01e-2  0.186   0.0928  4.52e-3  5.01e-1  1.00    2173.
 9 lambda[8]   1.62e-1  1.52e-1  0.0671  0.0650  6.91e-2  2.87e-1  1.00    2698.
10 lambda[9]   3.95e-1  3.50e-1  0.219   0.192   1.24e-1  8.12e-1  1.00    2264.
# ℹ 9,951 more rows
# ℹ 1 more variable: ess_tail <num>

We have some basic HMC-based validity statistics we can check.

Code

pnbd_short_fixed1_stanfit$cmdstan_diagnose()

Processing csv files: /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed1-1.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed1-2.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed1-3.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed1-4.csvWarning: non-fatal error reading adaptation data


Checking sampler transitions treedepth.
Treedepth satisfactory for all transitions.

Checking sampler transitions for divergences.
No divergent transitions found.

Checking E-BFMI - sampler transitions HMC potential energy.
E-BFMI satisfactory.

Effective sample size satisfactory.

Split R-hat values satisfactory all parameters.

Processing complete, no problems detected.

2.2 Visual Diagnostics of the Sample Validity

Now that we have a sample from the posterior distribution we need to create a few different visualisations of the diagnostics.

Code

parameter_subset <- c(
  "lambda[1]", "lambda[2]", "lambda[3]", "lambda[4]",
  "mu[1]",     "mu[2]",     "mu[3]",     "mu[4]"
  )

pnbd_short_fixed1_stanfit$draws(inc_warmup = FALSE) |>
  mcmc_trace(pars = parameter_subset) +
  expand_limits(y = 0) +
  labs(
    x = "Iteration",
    y = "Value",
    title = "Traceplot of Sample of Lambda and Mu Values"
    ) +
  theme(axis.text.x = element_text(size = 10))

We also check \(N_{eff}\) as a quick diagnostic of the fit.

Code

pnbd_short_fixed1_stanfit |>
  neff_ratio(pars = c("lambda", "mu")) |>
  mcmc_neff() +
    ggtitle("Plot of Parameter Effective Sample Sizes")

2.3 Assess the Model

As we intend to run the same logic to assess each of our models, we have combined all this logic into a single function run_model_assessment, to run the simulations and combine the datasets.

We first run the assessment data.

Code

pnbd_stanfit <- pnbd_short_fixed1_stanfit |>
  recover_types(customer_fit_stats_tbl)

pnbd_short_fixed1_assess_data_lst <- run_model_assessment(
  model_stanfit       = pnbd_stanfit,
  insample_tbl        = customer_fit_subset_tbl,
  fit_label           = "pnbd_short_fixed1",
  fit_end_dttm        = use_fit_end_date     |> as.POSIXct(),
  valid_start_dttm    = use_valid_start_date |> as.POSIXct(),
  valid_end_dttm      = use_valid_end_date   |> as.POSIXct(),
  precompute_rootdir  = "precompute",
  data_dir            = "data",
  summary_include_tnx = FALSE,
  sim_seed            = 10
  )

pnbd_short_fixed1_assess_data_lst |> glimpse()

List of 5
 $ model_fit_index_filepath     : 'glue' chr "data/pnbd_short_fixed1_assess_fit_index_tbl.rds"
 $ model_valid_index_filepath   : 'glue' chr "data/pnbd_short_fixed1_assess_valid_index_tbl.rds"
 $ model_simstats_filepath      : 'glue' chr "data/pnbd_short_fixed1_assess_model_simstats_tbl.rds"
 $ model_fit_simstats_filepath  : 'glue' chr "data/pnbd_short_fixed1_assess_fit_simstats_tbl.rds"
 $ model_valid_simstats_filepath: 'glue' chr "data/pnbd_short_fixed1_assess_valid_simstats_tbl.rds"

2.3.1 Check In-Sample Data Validation

We first check the model against the in-sample data.

Code

simdata_tbl <- pnbd_short_fixed1_assess_data_lst |>
  use_series(model_fit_simstats_filepath) |>
  read_rds()

insample_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_fit_subset_tbl,
  simdata_tbl = simdata_tbl
  )

insample_plots_lst$multi_plot |> print()

Code

insample_plots_lst$total_plot |> print()

Code

insample_plots_lst$quant_plot |> print()

This fit looks reasonable and appears to capture most of the aspects of the data used to fit it. Given that this is a synthetic dataset, this is not surprising, but at least we appreciate that our model is valid.

2.3.2 Check Out-of-Sample Data Validation

We now repeat for the out-of-sample data.

Code

simdata_tbl <- pnbd_short_fixed1_assess_data_lst |>
  use_series(model_valid_simstats_filepath) |>
  read_rds()

outsample_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_valid_subset_tbl,
  simdata_tbl = simdata_tbl
  )

outsample_plots_lst$multi_plot |> print()

Code

outsample_plots_lst$total_plot |> print()

Code

outsample_plots_lst$quant_plot |> print()

3 Fit Alternate Prior Model.

We want to try an alternate prior model with a smaller co-efficient of variation to see what impact it has on our procedures.

Code

stan_modelname <- "pnbd_short_fixed2"
stanfit_seed   <- stanfit_seed + 1
stanfit_prefix <- str_c("fit_", stan_modelname) 

stanfit_object_file <- glue("data/{stanfit_prefix}_stanfit.rds")


stan_data_lst <- customer_fit_stats_tbl |>
  select(customer_id, x, t_x, T_cal) |>
  compose_data(
    lambda_mn = 0.25,
    lambda_cv = 0.50,
    
    mu_mn     = 0.10,
    mu_cv     = 0.50,
    )

if(!file_exists(stanfit_object_file)) {
  pnbd_short_fixed2_stanfit <- pnbd_fixed_stanmodel$sample(
    data            =                stan_data_lst,
    chains          =                            4,
    iter_warmup     =                          500,
    iter_sampling   =                          500,
    seed            =                 stanfit_seed,
    save_warmup     =                         TRUE,
    output_dir      =                stan_modeldir,
    output_basename =               stanfit_prefix,
    )

  pnbd_short_fixed2_stanfit$save_object(stanfit_object_file, compress = "gzip")

} else {
  pnbd_short_fixed2_stanfit <- read_rds(stanfit_object_file)
}

pnbd_short_fixed2_stanfit$summary()

# A tibble: 9,961 × 10
   variable       mean   median      sd     mad       q5      q95  rhat ess_bulk
   <chr>         <num>    <num>   <num>   <num>    <num>    <num> <num>    <num>
 1 lp__       -1.10e+5 -1.10e+5 59.5    60.8    -1.10e+5 -1.10e+5  1.00     602.
 2 lambda[1]   3.69e-1  3.59e-1  0.107   0.102   2.20e-1  5.65e-1  1.00    4075.
 3 lambda[2]   2.27e-1  2.12e-1  0.0950  0.0931  9.74e-2  4.03e-1  1.00    4212.
 4 lambda[3]   2.49e-1  2.30e-1  0.118   0.109   9.62e-2  4.60e-1  1.00    4550.
 5 lambda[4]   2.10e-1  1.91e-1  0.110   0.102   7.00e-2  4.13e-1  1.00    4672.
 6 lambda[5]   3.38e-1  3.18e-1  0.135   0.124   1.56e-1  5.94e-1  1.00    4808.
 7 lambda[6]   2.45e-1  2.27e-1  0.117   0.107   8.78e-2  4.66e-1  1.01    4067.
 8 lambda[7]   2.12e-1  1.94e-1  0.111   0.0995  6.88e-2  4.15e-1  1.00    3742.
 9 lambda[8]   1.88e-1  1.81e-1  0.0646  0.0658  9.58e-2  3.01e-1  1.00    4541.
10 lambda[9]   3.13e-1  2.99e-1  0.121   0.117   1.45e-1  5.33e-1  1.00    3819.
# ℹ 9,951 more rows
# ℹ 1 more variable: ess_tail <num>

We have some basic HMC-based validity statistics we can check.

Code

pnbd_short_fixed2_stanfit$cmdstan_diagnose()

Processing csv files: /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed2-1.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed2-2.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed2-3.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed2-4.csvWarning: non-fatal error reading adaptation data


Checking sampler transitions treedepth.
Treedepth satisfactory for all transitions.

Checking sampler transitions for divergences.
No divergent transitions found.

Checking E-BFMI - sampler transitions HMC potential energy.
E-BFMI satisfactory.

Effective sample size satisfactory.

Split R-hat values satisfactory all parameters.

Processing complete, no problems detected.

3.1 Visual Diagnostics of the Sample Validity

Now that we have a sample from the posterior distribution we need to create a few different visualisations of the diagnostics.

Code

parameter_subset <- c(
  "lambda[1]", "lambda[2]", "lambda[3]", "lambda[4]",
  "mu[1]",     "mu[2]",     "mu[3]",     "mu[4]"
  )

pnbd_short_fixed2_stanfit$draws(inc_warmup = FALSE) |>
  mcmc_trace(pars = parameter_subset) +
  expand_limits(y = 0) +
  labs(
    x = "Iteration",
    y = "Value",
    title = "Traceplot of Sample of Lambda and Mu Values"
    ) +
  theme(axis.text.x = element_text(size = 10))

We want to check the \(N_{eff}\) statistics also.

Code

pnbd_short_fixed2_stanfit |>
  neff_ratio(pars = c("lambda", "mu")) |>
  mcmc_neff() +
    ggtitle("Plot of Parameter Effective Sample Sizes")

3.2 Assess the Model

As we intend to run the same logic to assess each of our models, we have combined all this logic into a single function run_model_assessment, to run the simulations and combine the datasets.

We first run the assessment data.

Code

pnbd_stanfit <- pnbd_short_fixed2_stanfit |>
  recover_types(customer_fit_stats_tbl)

pnbd_short_fixed2_assess_data_lst <- run_model_assessment(
  model_stanfit       = pnbd_stanfit,
  insample_tbl        = customer_fit_subset_tbl,
  fit_label           = "pnbd_short_fixed2",
  fit_end_dttm        = use_fit_end_date     |> as.POSIXct(),
  valid_start_dttm    = use_valid_start_date |> as.POSIXct(),
  valid_end_dttm      = use_valid_end_date   |> as.POSIXct(),
  precompute_rootdir  = "precompute",
  data_dir            = "data",
  summary_include_tnx = FALSE,
  sim_seed            = 20
  )

pnbd_short_fixed2_assess_data_lst |> glimpse()

List of 5
 $ model_fit_index_filepath     : 'glue' chr "data/pnbd_short_fixed2_assess_fit_index_tbl.rds"
 $ model_valid_index_filepath   : 'glue' chr "data/pnbd_short_fixed2_assess_valid_index_tbl.rds"
 $ model_simstats_filepath      : 'glue' chr "data/pnbd_short_fixed2_assess_model_simstats_tbl.rds"
 $ model_fit_simstats_filepath  : 'glue' chr "data/pnbd_short_fixed2_assess_fit_simstats_tbl.rds"
 $ model_valid_simstats_filepath: 'glue' chr "data/pnbd_short_fixed2_assess_valid_simstats_tbl.rds"

3.2.1 Check In-Sample Data Validation

We first check the model against the in-sample data.

Code

simdata_tbl <- pnbd_short_fixed2_assess_data_lst |>
  use_series(model_fit_simstats_filepath) |>
  read_rds()

insample_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_fit_subset_tbl,
  simdata_tbl = simdata_tbl
  )

insample_plots_lst$multi_plot |> print()

Code

insample_plots_lst$total_plot |> print()

Code

insample_plots_lst$quant_plot |> print()

This fit looks reasonable and appears to capture most of the aspects of the data used to fit it. Given that this is a synthetic dataset, this is not surprising, but at least we appreciate that our model is valid.

3.2.2 Check Out-of-Sample Data Validation

We now repeat for the out-of-sample data.

Code

simdata_tbl <- pnbd_short_fixed2_assess_data_lst |>
  use_series(model_valid_simstats_filepath) |>
  read_rds()

outsample_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_valid_subset_tbl,
  simdata_tbl = simdata_tbl
  )

outsample_plots_lst$multi_plot |> print()

Code

outsample_plots_lst$total_plot |> print()

Code

outsample_plots_lst$quant_plot |> print()

4 Fit Tight-Lifetime Model

We now want to try a model where we use priors with a tighter coefficient of variation for lifetime but keep the CoV for transaction frequency.

Code

stan_modelname <- "pnbd_short_fixed3"
stanfit_seed   <- stanfit_seed + 1
stanfit_prefix <- str_c("fit_", stan_modelname) 

stanfit_object_file <- glue("data/{stanfit_prefix}_stanfit.rds")


stan_data_lst <- customer_fit_stats_tbl |>
  select(customer_id, x, t_x, T_cal) |>
  compose_data(
    lambda_mn = 0.25,
    lambda_cv = 1.00,
    
    mu_mn     = 0.10,
    mu_cv     = 0.50,
    )

if(!file_exists(stanfit_object_file)) {
  pnbd_short_fixed3_stanfit <- pnbd_fixed_stanmodel$sample(
    data            =                stan_data_lst,
    chains          =                            4,
    iter_warmup     =                          500,
    iter_sampling   =                          500,
    seed            =                 stanfit_seed,
    save_warmup     =                         TRUE,
    output_dir      =                stan_modeldir,
    output_basename =               stanfit_prefix,
    )

  pnbd_short_fixed3_stanfit$save_object(stanfit_object_file, compress = "gzip")

} else {
  pnbd_short_fixed3_stanfit <- read_rds(stanfit_object_file)
}
  
pnbd_short_fixed3_stanfit$summary()

# A tibble: 9,961 × 10
   variable       mean   median      sd     mad       q5      q95  rhat ess_bulk
   <chr>         <num>    <num>   <num>   <num>    <num>    <num> <num>    <num>
 1 lp__       -8.50e+4 -8.50e+4 61.6    62.6    -8.51e+4 -8.49e+4  1.00     587.
 2 lambda[1]   4.49e-1  4.33e-1  0.150   0.142   2.40e-1  7.17e-1  1.00    3162.
 3 lambda[2]   2.10e-1  1.82e-1  0.128   0.119   5.44e-2  4.53e-1  1.00    2741.
 4 lambda[3]   2.56e-1  2.01e-1  0.205   0.157   3.78e-2  6.66e-1  1.00    3078.
 5 lambda[4]   1.34e-1  7.83e-2  0.159   0.0878  5.17e-3  4.51e-1  1.00    1997.
 6 lambda[5]   4.85e-1  4.45e-1  0.256   0.242   1.49e-1  9.71e-1  1.00    2727.
 7 lambda[6]   2.40e-1  1.90e-1  0.194   0.153   3.11e-2  6.12e-1  1.00    2271.
 8 lambda[7]   1.42e-1  8.73e-2  0.165   0.0966  5.30e-3  4.71e-1  1.00    2557.
 9 lambda[8]   1.64e-1  1.57e-1  0.0667  0.0633  7.10e-2  2.82e-1  1.00    2656.
10 lambda[9]   3.98e-1  3.62e-1  0.210   0.186   1.29e-1  7.98e-1  1.01    3068.
# ℹ 9,951 more rows
# ℹ 1 more variable: ess_tail <num>

We have some basic HMC-based validity statistics we can check.

Code

pnbd_short_fixed3_stanfit$cmdstan_diagnose()

Processing csv files: /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed3-1.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed3-2.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed3-3.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed3-4.csvWarning: non-fatal error reading adaptation data


Checking sampler transitions treedepth.
Treedepth satisfactory for all transitions.

Checking sampler transitions for divergences.
No divergent transitions found.

Checking E-BFMI - sampler transitions HMC potential energy.
E-BFMI satisfactory.

Effective sample size satisfactory.

Split R-hat values satisfactory all parameters.

Processing complete, no problems detected.

4.1 Visual Diagnostics of the Sample Validity

Now that we have a sample from the posterior distribution we need to create a few different visualisations of the diagnostics.

Code

parameter_subset <- c(
  "lambda[1]", "lambda[2]", "lambda[3]", "lambda[4]",
  "mu[1]",     "mu[2]",     "mu[3]",     "mu[4]"
  )

pnbd_short_fixed3_stanfit$draws(inc_warmup = FALSE) |>
  mcmc_trace(pars = parameter_subset) +
  expand_limits(y = 0) +
  labs(
    x = "Iteration",
    y = "Value",
    title = "Traceplot of Sample of Lambda and Mu Values"
    ) +
  theme(axis.text.x = element_text(size = 10))

We want to check the \(N_{eff}\) statistics also.

Code

pnbd_short_fixed3_stanfit |>
  neff_ratio(pars = c("lambda", "mu")) |>
  mcmc_neff() +
    ggtitle("Plot of Parameter Effective Sample Sizes")

4.2 Assess the Model

As we intend to run the same logic to assess each of our models, we have combined all this logic into a single function run_model_assessment, to run the simulations and combine the datasets.

We first run the assessment data.

Code

pnbd_stanfit <- pnbd_short_fixed3_stanfit |>
  recover_types(customer_fit_stats_tbl)

pnbd_short_fixed3_assess_data_lst <- run_model_assessment(
  model_stanfit       = pnbd_stanfit,
  insample_tbl        = customer_fit_subset_tbl,
  fit_label           = "pnbd_short_fixed3",
  fit_end_dttm        = use_fit_end_date     |> as.POSIXct(),
  valid_start_dttm    = use_valid_start_date |> as.POSIXct(),
  valid_end_dttm      = use_valid_end_date   |> as.POSIXct(),
  precompute_rootdir  = "precompute",
  data_dir            = "data",
  summary_include_tnx = FALSE,
  sim_seed            = 30
  )

pnbd_short_fixed3_assess_data_lst |> glimpse()

List of 5
 $ model_fit_index_filepath     : 'glue' chr "data/pnbd_short_fixed3_assess_fit_index_tbl.rds"
 $ model_valid_index_filepath   : 'glue' chr "data/pnbd_short_fixed3_assess_valid_index_tbl.rds"
 $ model_simstats_filepath      : 'glue' chr "data/pnbd_short_fixed3_assess_model_simstats_tbl.rds"
 $ model_fit_simstats_filepath  : 'glue' chr "data/pnbd_short_fixed3_assess_fit_simstats_tbl.rds"
 $ model_valid_simstats_filepath: 'glue' chr "data/pnbd_short_fixed3_assess_valid_simstats_tbl.rds"

4.2.1 Check In-Sample Data Validation

We first check the model against the in-sample data.

Code

simdata_tbl <- pnbd_short_fixed3_assess_data_lst |>
  use_series(model_fit_simstats_filepath) |>
  read_rds()

insample_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_fit_subset_tbl,
  simdata_tbl = simdata_tbl
  )

insample_plots_lst$multi_plot |> print()

Code

insample_plots_lst$total_plot |> print()

Code

insample_plots_lst$quant_plot |> print()

This fit looks reasonable and appears to capture most of the aspects of the data used to fit it. Given that this is a synthetic dataset, this is not surprising, but at least we appreciate that our model is valid.

4.2.2 Check Out-of-Sample Data Validation

We now repeat for the out-of-sample data.

Code

simdata_tbl <- pnbd_short_fixed3_assess_data_lst |>
  use_series(model_valid_simstats_filepath) |>
  read_rds()

outsample_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_valid_subset_tbl,
  simdata_tbl = simdata_tbl
  )

outsample_plots_lst$multi_plot |> print()

Code

outsample_plots_lst$total_plot |> print()

Code

outsample_plots_lst$quant_plot |> print()

5 Fit Narrow-Short-Lifetime Model

We now want to try a model where we use priors with a tighter coefficient of variation for lifetime but keep the CoV for transaction frequency.

Code

stan_modelname <- "pnbd_short_fixed4"
stanfit_seed   <- stanfit_seed + 1
stanfit_prefix <- str_c("fit_", stan_modelname) 

stanfit_object_file <- glue("data/{stanfit_prefix}_stanfit.rds")


stan_data_lst <- customer_fit_stats_tbl |>
  select(customer_id, x, t_x, T_cal) |>
  compose_data(
    lambda_mn = 0.25,
    lambda_cv = 1.00,
    
    mu_mn     = 0.20,
    mu_cv     = 0.30,
    )

if(!file_exists(stanfit_object_file)) {
  pnbd_short_fixed4_stanfit <- pnbd_fixed_stanmodel$sample(
    data            =                stan_data_lst,
    chains          =                            4,
    iter_warmup     =                          500,
    iter_sampling   =                          500,
    seed            =                 stanfit_seed,
    save_warmup     =                         TRUE,
    output_dir      =                stan_modeldir,
    output_basename =               stanfit_prefix,
    )

  pnbd_short_fixed4_stanfit$save_object(stanfit_object_file, compress = "gzip")

} else {
  pnbd_short_fixed4_stanfit <- read_rds(stanfit_object_file)
}

pnbd_short_fixed4_stanfit$summary()

# A tibble: 9,961 × 10
   variable       mean   median      sd     mad       q5      q95  rhat ess_bulk
   <chr>         <num>    <num>   <num>   <num>    <num>    <num> <num>    <num>
 1 lp__       -1.39e+5 -1.39e+5 59.5    58.6    -1.39e+5 -1.39e+5  1.00     768.
 2 lambda[1]   4.54e-1  4.34e-1  0.156   0.154   2.31e-1  7.36e-1  1.00    3432.
 3 lambda[2]   2.24e-1  1.94e-1  0.147   0.122   4.91e-2  5.04e-1  1.00    2935.
 4 lambda[3]   2.79e-1  2.24e-1  0.210   0.173   4.57e-2  6.74e-1  1.00    3045.
 5 lambda[4]   1.51e-1  1.01e-1  0.162   0.104   7.20e-3  4.48e-1  1.00    2366.
 6 lambda[5]   5.02e-1  4.53e-1  0.271   0.247   1.54e-1  1.01e+0  1.00    3307.
 7 lambda[6]   2.63e-1  2.16e-1  0.199   0.174   3.74e-2  6.73e-1  1.00    2378.
 8 lambda[7]   1.62e-1  1.02e-1  0.176   0.108   7.47e-3  5.29e-1  1.00    2490.
 9 lambda[8]   1.70e-1  1.60e-1  0.0714  0.0668  7.37e-2  2.98e-1  1.01    2918.
10 lambda[9]   4.16e-1  3.78e-1  0.232   0.214   1.20e-1  8.58e-1  1.00    2779.
# ℹ 9,951 more rows
# ℹ 1 more variable: ess_tail <num>

We have some basic HMC-based validity statistics we can check.

Code

pnbd_short_fixed4_stanfit$cmdstan_diagnose()

Processing csv files: /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed4-1.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed4-2.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed4-3.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_short_fixed4-4.csvWarning: non-fatal error reading adaptation data


Checking sampler transitions treedepth.
Treedepth satisfactory for all transitions.

Checking sampler transitions for divergences.
No divergent transitions found.

Checking E-BFMI - sampler transitions HMC potential energy.
E-BFMI satisfactory.

Effective sample size satisfactory.

Split R-hat values satisfactory all parameters.

Processing complete, no problems detected.

5.1 Visual Diagnostics of the Sample Validity

Now that we have a sample from the posterior distribution we need to create a few different visualisations of the diagnostics.

Code

parameter_subset <- c(
  "lambda[1]", "lambda[2]", "lambda[3]", "lambda[4]",
  "mu[1]",     "mu[2]",     "mu[3]",     "mu[4]"
  )

pnbd_short_fixed4_stanfit$draws(inc_warmup = FALSE) |>
  mcmc_trace(pars = parameter_subset) +
  expand_limits(y = 0) +
  labs(
    x = "Iteration",
    y = "Value",
    title = "Traceplot of Sample of Lambda and Mu Values"
    ) +
  theme(axis.text.x = element_text(size = 10))

We want to check the \(N_{eff}\) statistics also.

Code

pnbd_short_fixed4_stanfit |>
  neff_ratio(pars = c("lambda", "mu")) |>
  mcmc_neff() +
    ggtitle("Plot of Parameter Effective Sample Sizes")

5.2 Assess the Model

As we intend to run the same logic to assess each of our models, we have combined all this logic into a single function run_model_assessment, to run the simulations and combine the datasets.

We first run the assessment data.

Code

pnbd_stanfit <- pnbd_short_fixed4_stanfit |>
  recover_types(customer_fit_stats_tbl)

pnbd_short_fixed4_assess_data_lst <- run_model_assessment(
  model_stanfit       = pnbd_stanfit,
  insample_tbl        = customer_fit_subset_tbl,
  fit_label           = "pnbd_short_fixed4",
  fit_end_dttm        = use_fit_end_date     |> as.POSIXct(),
  valid_start_dttm    = use_valid_start_date |> as.POSIXct(),
  valid_end_dttm      = use_valid_end_date   |> as.POSIXct(),
  precompute_rootdir  = "precompute",
  data_dir            = "data",
  summary_include_tnx = FALSE,
  sim_seed            = 40
  )

pnbd_short_fixed4_assess_data_lst |> glimpse()

List of 5
 $ model_fit_index_filepath     : 'glue' chr "data/pnbd_short_fixed4_assess_fit_index_tbl.rds"
 $ model_valid_index_filepath   : 'glue' chr "data/pnbd_short_fixed4_assess_valid_index_tbl.rds"
 $ model_simstats_filepath      : 'glue' chr "data/pnbd_short_fixed4_assess_model_simstats_tbl.rds"
 $ model_fit_simstats_filepath  : 'glue' chr "data/pnbd_short_fixed4_assess_fit_simstats_tbl.rds"
 $ model_valid_simstats_filepath: 'glue' chr "data/pnbd_short_fixed4_assess_valid_simstats_tbl.rds"

5.2.1 Check In-Sample Data Validation

We first check the model against the in-sample data.

Code

simdata_tbl <- pnbd_short_fixed4_assess_data_lst |>
  use_series(model_fit_simstats_filepath) |>
  read_rds()

insample_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_fit_subset_tbl,
  simdata_tbl = simdata_tbl
  )

insample_plots_lst$multi_plot |> print()

Code

insample_plots_lst$total_plot |> print()

Code

insample_plots_lst$quant_plot |> print()

This fit looks reasonable and appears to capture most of the aspects of the data used to fit it. Given that this is a synthetic dataset, this is not surprising, but at least we appreciate that our model is valid.

5.2.2 Check Out-of-Sample Data Validation

We now repeat for the out-of-sample data.

Code

simdata_tbl <- pnbd_short_fixed4_assess_data_lst |>
  use_series(model_valid_simstats_filepath) |>
  read_rds()

outsample_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_valid_subset_tbl,
  simdata_tbl = simdata_tbl
  )

outsample_plots_lst$multi_plot |> print()

Code

outsample_plots_lst$total_plot |> print()

Code

outsample_plots_lst$quant_plot |> print()

6 Compare Model Outputs

We have looked at each of the models individually, but it is also worth looking at each of the models as a group.

Code

calculate_simulation_statistics <- function(file_rds) {
  simdata_tbl <- read_rds(file_rds)
  
  multicount_cust_tbl <- simdata_tbl |>
    filter(sim_tnx_count > 0) |>
    count(draw_id, name = "multicust_count")
  
  totaltnx_data_tbl <- simdata_tbl |>
    count(draw_id, wt = sim_tnx_count, name = "simtnx_count")
  
  simstats_tbl <- multicount_cust_tbl |>
    inner_join(totaltnx_data_tbl, by = "draw_id")
  
  return(simstats_tbl)
}

Code

obs_fit_customer_count <- customer_fit_subset_tbl |>
  filter(tnx_count > 0) |>
  nrow()

obs_valid_customer_count <- customer_valid_subset_tbl |>
  filter(tnx_count > 0) |>
  nrow()

obs_fit_total_count <- customer_fit_subset_tbl |>
  pull(tnx_count) |>
  sum()

obs_valid_total_count <- customer_valid_subset_tbl |>
  pull(tnx_count) |>
  sum()


obs_stats_tbl <- tribble(
  ~assess_type, ~name,               ~obs_value,
  "fit",        "multicust_count",   obs_fit_customer_count,
  "fit",        "simtnx_count",      obs_fit_total_count,
  "valid",      "multicust_count",   obs_valid_customer_count,
  "valid",      "simtnx_count",      obs_valid_total_count
  )


model_assess_tbl <- dir_ls("data", regexp = "pnbd_short_fixed.*_assess_.*simstats") |>
  enframe(name = NULL, value = "file_path") |>
  filter(str_detect(file_path, "_assess_model_", negate = TRUE)) |>
  mutate(
    model_label = str_replace(file_path, "data/pnbd_short_(.*?)_assess_.*", "\\1"),
    assess_type = if_else(str_detect(file_path, "_assess_fit_"), "fit", "valid"),
    
    sim_data = map(
      file_path, calculate_simulation_statistics,
      
      .progress = "calculate_simulation_statistics"
      )
    )

model_assess_tbl |> glimpse()

Rows: 8
Columns: 4
$ file_path   <fs::path> "data/pnbd_short_fixed1_assess_fit_simstats_tbl.rds",…
$ model_label <chr> "fixed1", "fixed1", "fixed2", "fixed2", "fixed3", "fixed3"…
$ assess_type <chr> "fit", "valid", "fit", "valid", "fit", "valid", "fit", "va…
$ sim_data    <list> [<tbl_df[2000 x 3]>], [<tbl_df[2000 x 3]>], [<tbl_df[2000…

Code

model_assess_summstat_tbl <- model_assess_tbl |>
  select(model_label, assess_type, sim_data) |>
  unnest(sim_data) |>
  pivot_longer(
    cols = !c(model_label, assess_type, draw_id)
    ) |>
  group_by(model_label, assess_type, name) |>
  summarise(
    .groups = "drop",
    
    mean_val = mean(value),
    p10 = quantile(value, 0.10),
    p25 = quantile(value, 0.25),
    p50 = quantile(value, 0.50),
    p75 = quantile(value, 0.75),
    p90 = quantile(value, 0.90)
    )

model_assess_summstat_tbl |> glimpse()

Rows: 16
Columns: 9
$ model_label <chr> "fixed1", "fixed1", "fixed1", "fixed1", "fixed2", "fixed2"…
$ assess_type <chr> "fit", "fit", "valid", "valid", "fit", "fit", "valid", "va…
$ name        <chr> "multicust_count", "simtnx_count", "multicust_count", "sim…
$ mean_val    <dbl> 601.6880, 4081.1590, 158.9110, 1559.5810, 671.4355, 3094.8…
$ p10         <dbl> 583.0, 3819.0, 149.0, 1399.0, 653.0, 2907.9, 110.9, 686.0,…
$ p25         <dbl> 592.00, 3936.00, 153.00, 1470.00, 662.00, 2996.00, 115.00,…
$ p50         <dbl> 602.0, 4079.0, 159.0, 1553.0, 672.0, 3095.0, 119.0, 787.0,…
$ p75         <dbl> 612, 4220, 165, 1647, 681, 3194, 124, 842, 596, 3164, 119,…
$ p90         <dbl> 620.0, 4357.0, 169.0, 1733.1, 689.0, 3282.0, 128.0, 897.0,…

Code

#! echo: TRUE

ggplot(model_assess_summstat_tbl) +
  geom_errorbar(
    aes(x = model_label, ymin = p10, ymax = p90), width = 0
    ) +
  geom_errorbar(
    aes(x = model_label, ymin = p25, ymax = p75), width = 0, linewidth = 3
    ) +
  geom_hline(
    aes(yintercept = obs_value),
    data = obs_stats_tbl, colour = "red"
    ) +
  scale_y_continuous(labels = label_comma()) +
  expand_limits(y = 0) +
  facet_wrap(
    vars(assess_type, name), scale = "free_y"
    ) +
  labs(
    x = "Model",
    y = "Count",
    title = "Comparison Plot for the Different Models"
    ) +
  theme(
    axis.text.x = element_text(angle = 20, vjust = 0.5, size = 8)
    )

6.1 Write Assessment Data to Disk

We now want to save the assessment data to disk.

Code

model_assess_tbl |> write_rds("data/assess_data_pnbd_short_fixed_tbl.rds")

R Environment

Code

options(width = 120L)
sessioninfo::session_info()

─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.1 (2023-06-16)
 os       Ubuntu 22.04.3 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Dublin
 date     2023-11-11
 pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package        * version    date (UTC) lib source
 abind            1.4-5      2016-07-21 [1] RSPM (R 4.3.0)
 arrayhelpers     1.1-0      2020-02-04 [1] RSPM (R 4.3.0)
 backports        1.4.1      2021-12-13 [1] RSPM (R 4.3.0)
 base64enc        0.1-3      2015-07-28 [1] RSPM (R 4.3.0)
 bayesplot      * 1.10.0     2022-11-16 [1] RSPM (R 4.3.0)
 bit              4.0.5      2022-11-15 [1] RSPM (R 4.3.0)
 bit64            4.0.5      2020-08-30 [1] RSPM (R 4.3.0)
 bridgesampling   1.1-2      2021-04-16 [1] RSPM (R 4.3.0)
 brms           * 2.20.4     2023-09-25 [1] RSPM (R 4.3.0)
 Brobdingnag      1.2-9      2022-10-19 [1] RSPM (R 4.3.0)
 cachem           1.0.8      2023-05-01 [1] RSPM (R 4.3.0)
 callr            3.7.3      2022-11-02 [1] RSPM (R 4.3.0)
 checkmate        2.3.0      2023-10-25 [1] RSPM (R 4.3.0)
 cli              3.6.1      2023-03-23 [1] RSPM (R 4.3.0)
 cmdstanr       * 0.6.0.9000 2023-11-07 [1] Github (stan-dev/cmdstanr@a13c798)
 coda             0.19-4     2020-09-30 [1] RSPM (R 4.3.0)
 codetools        0.2-19     2023-02-01 [2] CRAN (R 4.3.1)
 colorspace       2.1-0      2023-01-23 [1] RSPM (R 4.3.0)
 colourpicker     1.3.0      2023-08-21 [1] RSPM (R 4.3.0)
 conflicted     * 1.2.0      2023-02-01 [1] RSPM (R 4.3.0)
 cowplot        * 1.1.1      2020-12-30 [1] RSPM (R 4.3.0)
 crayon           1.5.2      2022-09-29 [1] RSPM (R 4.3.0)
 crosstalk        1.2.0      2021-11-04 [1] RSPM (R 4.3.0)
 curl             5.1.0      2023-10-02 [1] RSPM (R 4.3.0)
 digest           0.6.33     2023-07-07 [1] RSPM (R 4.3.0)
 directlabels   * 2023.8.25  2023-09-01 [1] RSPM (R 4.3.0)
 distributional   0.3.2      2023-03-22 [1] RSPM (R 4.3.0)
 dplyr          * 1.1.3      2023-09-03 [1] RSPM (R 4.3.0)
 DT               0.30       2023-10-05 [1] RSPM (R 4.3.0)
 dygraphs         1.1.1.6    2018-07-11 [1] RSPM (R 4.3.0)
 ellipsis         0.3.2      2021-04-29 [1] RSPM (R 4.3.0)
 evaluate         0.22       2023-09-29 [1] RSPM (R 4.3.0)
 fansi            1.0.5      2023-10-08 [1] RSPM (R 4.3.0)
 farver           2.1.1      2022-07-06 [1] RSPM (R 4.3.0)
 fastmap          1.1.1      2023-02-24 [1] RSPM (R 4.3.0)
 forcats        * 1.0.0      2023-01-29 [1] RSPM (R 4.3.0)
 fs             * 1.6.3      2023-07-20 [1] RSPM (R 4.3.0)
 furrr          * 0.3.1      2022-08-15 [1] RSPM (R 4.3.0)
 future         * 1.33.0     2023-07-01 [1] RSPM (R 4.3.0)
 generics         0.1.3      2022-07-05 [1] RSPM (R 4.3.0)
 ggdist           3.3.0      2023-05-13 [1] RSPM (R 4.3.0)
 ggplot2        * 3.4.4      2023-10-12 [1] RSPM (R 4.3.0)
 globals          0.16.2     2022-11-21 [1] RSPM (R 4.3.0)
 glue           * 1.6.2      2022-02-24 [1] RSPM (R 4.3.0)
 gridExtra        2.3        2017-09-09 [1] RSPM (R 4.3.0)
 gtable           0.3.4      2023-08-21 [1] RSPM (R 4.3.0)
 gtools           3.9.4      2022-11-27 [1] RSPM (R 4.3.0)
 hms              1.1.3      2023-03-21 [1] RSPM (R 4.3.0)
 htmltools        0.5.6.1    2023-10-06 [1] RSPM (R 4.3.0)
 htmlwidgets      1.6.2      2023-03-17 [1] RSPM (R 4.3.0)
 httpuv           1.6.12     2023-10-23 [1] RSPM (R 4.3.0)
 igraph           1.5.1      2023-08-10 [1] RSPM (R 4.3.0)
 inline           0.3.19     2021-05-31 [1] RSPM (R 4.3.0)
 jsonlite         1.8.7      2023-06-29 [1] RSPM (R 4.3.0)
 knitr            1.44       2023-09-11 [1] RSPM (R 4.3.0)
 labeling         0.4.3      2023-08-29 [1] RSPM (R 4.3.0)
 later            1.3.1      2023-05-02 [1] RSPM (R 4.3.0)
 lattice          0.21-8     2023-04-05 [2] CRAN (R 4.3.1)
 lifecycle        1.0.3      2022-10-07 [1] RSPM (R 4.3.0)
 listenv          0.9.0      2022-12-16 [1] RSPM (R 4.3.0)
 loo              2.6.0      2023-03-31 [1] RSPM (R 4.3.0)
 lubridate      * 1.9.3      2023-09-27 [1] RSPM (R 4.3.0)
 magrittr       * 2.0.3      2022-03-30 [1] RSPM (R 4.3.0)
 markdown         1.11       2023-10-19 [1] RSPM (R 4.3.0)
 Matrix           1.5-4.1    2023-05-18 [2] CRAN (R 4.3.1)
 matrixStats      1.0.0      2023-06-02 [1] RSPM (R 4.3.0)
 memoise          2.0.1      2021-11-26 [1] RSPM (R 4.3.0)
 mime             0.12       2021-09-28 [1] RSPM (R 4.3.0)
 miniUI           0.1.1.1    2018-05-18 [1] RSPM (R 4.3.0)
 munsell          0.5.0      2018-06-12 [1] RSPM (R 4.3.0)
 mvtnorm          1.2-3      2023-08-25 [1] RSPM (R 4.3.0)
 nlme             3.1-162    2023-01-31 [2] CRAN (R 4.3.1)
 parallelly       1.36.0     2023-05-26 [1] RSPM (R 4.3.0)
 pillar           1.9.0      2023-03-22 [1] RSPM (R 4.3.0)
 pkgbuild         1.4.2      2023-06-26 [1] RSPM (R 4.3.0)
 pkgconfig        2.0.3      2019-09-22 [1] RSPM (R 4.3.0)
 plyr             1.8.9      2023-10-02 [1] RSPM (R 4.3.0)
 posterior      * 1.4.1      2023-03-14 [1] RSPM (R 4.3.0)
 prettyunits      1.2.0      2023-09-24 [1] RSPM (R 4.3.0)
 processx         3.8.2      2023-06-30 [1] RSPM (R 4.3.0)
 promises         1.2.1      2023-08-10 [1] RSPM (R 4.3.0)
 ps               1.7.5      2023-04-18 [1] RSPM (R 4.3.0)
 purrr          * 1.0.2      2023-08-10 [1] RSPM (R 4.3.0)
 quadprog         1.5-8      2019-11-20 [1] RSPM (R 4.3.0)
 QuickJSR         1.0.7      2023-10-15 [1] RSPM (R 4.3.0)
 R6               2.5.1      2021-08-19 [1] RSPM (R 4.3.0)
 Rcpp           * 1.0.11     2023-07-06 [1] RSPM (R 4.3.0)
 RcppParallel     5.1.7      2023-02-27 [1] RSPM (R 4.3.0)
 readr          * 2.1.4      2023-02-10 [1] RSPM (R 4.3.0)
 reshape2         1.4.4      2020-04-09 [1] RSPM (R 4.3.0)
 rlang          * 1.1.1      2023-04-28 [1] RSPM (R 4.3.0)
 rmarkdown        2.25       2023-09-18 [1] RSPM (R 4.3.0)
 rstan            2.32.3     2023-10-15 [1] RSPM (R 4.3.0)
 rstantools       2.3.1.1    2023-07-18 [1] RSPM (R 4.3.0)
 rstudioapi       0.15.0     2023-07-07 [1] RSPM (R 4.3.0)
 rsyslog        * 1.0.3      2023-05-08 [1] RSPM (R 4.3.0)
 scales         * 1.2.1      2022-08-20 [1] RSPM (R 4.3.0)
 sessioninfo      1.2.2      2021-12-06 [1] RSPM (R 4.3.0)
 shiny            1.7.5.1    2023-10-14 [1] RSPM (R 4.3.0)
 shinyjs          2.1.0      2021-12-23 [1] RSPM (R 4.3.0)
 shinystan        2.6.0      2022-03-03 [1] RSPM (R 4.3.0)
 shinythemes      1.2.0      2021-01-25 [1] RSPM (R 4.3.0)
 StanHeaders      2.26.28    2023-09-07 [1] RSPM (R 4.3.0)
 stringi          1.7.12     2023-01-11 [1] RSPM (R 4.3.0)
 stringr        * 1.5.0      2022-12-02 [1] RSPM (R 4.3.0)
 svUnit           1.0.6      2021-04-19 [1] RSPM (R 4.3.0)
 tensorA          0.36.2     2020-11-19 [1] RSPM (R 4.3.0)
 threejs          0.3.3      2020-01-21 [1] RSPM (R 4.3.0)
 tibble         * 3.2.1      2023-03-20 [1] RSPM (R 4.3.0)
 tidybayes      * 3.0.6      2023-08-12 [1] RSPM (R 4.3.0)
 tidyr          * 1.3.0      2023-01-24 [1] RSPM (R 4.3.0)
 tidyselect       1.2.0      2022-10-10 [1] RSPM (R 4.3.0)
 tidyverse      * 2.0.0      2023-02-22 [1] RSPM (R 4.3.0)
 timechange       0.2.0      2023-01-11 [1] RSPM (R 4.3.0)
 tzdb             0.4.0      2023-05-12 [1] RSPM (R 4.3.0)
 utf8             1.2.4      2023-10-22 [1] RSPM (R 4.3.0)
 V8               4.4.0      2023-10-09 [1] RSPM (R 4.3.0)
 vctrs            0.6.4      2023-10-12 [1] RSPM (R 4.3.0)
 vroom            1.6.4      2023-10-02 [1] RSPM (R 4.3.0)
 withr            2.5.1      2023-09-26 [1] RSPM (R 4.3.0)
 xfun             0.40       2023-08-09 [1] RSPM (R 4.3.0)
 xtable           1.8-4      2019-04-21 [1] RSPM (R 4.3.0)
 xts              0.13.1     2023-04-16 [1] RSPM (R 4.3.0)
 yaml             2.3.7      2023-01-23 [1] RSPM (R 4.3.0)
 zoo              1.8-12     2023-04-13 [1] RSPM (R 4.3.0)

 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library

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Code

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